Download St. Jude Faculty Mentors for the 2016

St. Jude Faculty Mentors for the 2016-2017 Summer Plus Fellowship
Richard Kriwacki, PhD
Member
Department: Structural Biology
Understanding the molecular basis for the liquid-like structure of the nucleolus, a
membrane-less organelle
In the Kriwacki laboratory, we strive to understand the molecular mechanisms utilized
by living cells to spatially organize macromolecules for specific biological processes. One level of
intracellular organization arises through a process called “phase separation”, akin to the oil-water
separation in, for example, vinegrette. Inside the cell, certain proteins and ribonucleic acids that initially
move freely in the nucleus or cytoplasm, come together through phase separation to form highly dense,
liquid-like bodies—these bodies are termed “membrane-less organelles”. Studies of membrane-less
organelles have recently emerged as important new branches of the fields of cellular and structural
biology. In particular, we are interested in how phase separation controls formation of the membraneless organelle called the nucleolus. The nucleolus is the ribosome-producing factory of the eukaryotic
cell and, importantly, defects in the function of the nucleolus are associated with serious diseases, such
as cancer and infectious diseases.
The nucleolus contains a staggering ~4,500 proteins, but the molecular mechanisms that control their
assembly are currently poorly understood. Recently, we discovered several types of molecular
“fingerprints” that cause proteins to go into the nucleolus. Furthermore, we demonstrated in the test
tube that molecular interactions between these different fingerprints cause phase separation into
liquid-like droplets. A Summer Plus student will have the opportunity to study how different nucleoloar
proteins sequentially assemble through phase separation to form the nucleolus. The fundamental
insights that will be gained from this study will provide a valuable foundation for the development of
novel therapeutic agents that selectively target diseased cells to restore normal nucleolar functions.
The study will involve measuring thermodynamic and kinetic parameters of inter-molecular interactions
between nucleolar proteins and how the interaction strength and association-dissociation rates
correlate with macroscopic properties of the liquid-like droplets. A basic understanding of chemistry
concepts is required for these studies. We utilize a variety of complementary laboratory techniques in
order to obtain insights into the molecular mechanisms that control macroscopic features of the liquidlike droplets. Below are a few techniques that you will have the opportunity to learn and apply in this
study:
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Produce recombinant human nucleolar proteins using the E. Coli bacterial expression system,
Purify recombinant proteins using a variety of chromatography-based techniques,
Probe intermolecular interactions using nucleic magnetic resonance (NMR) spectroscopy,
Measure interaction affinity using isothermal titration calorimetry (ITC),
Chemically conjugate proteins with fluorescent probes, and
Characterize the macroscopic features of liquid-like droplets using fluorescence microscopybased assays.
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Jamy C Peng, PhD
Assistant Member
Department: Developmental Neurobiology
My lab investigates epigenetic mechanisms that regulate stem cell functions, with a
specific focus on epigenetic factors Piwi and Polycomb Group proteins. Stem cells are
responsible for originating and maintaining most adult tissues in the human body.
Over proliferation of stem cells can cause cancer, and under proliferation of stem cells
leads to a variety of diseases such as tissue dystrophy, immuno-deficiency, and even death. Therefore,
understanding stem cell regulation would contribute to understanding of human health and disease.
Epigenetic factors are chromatin-associated proteins or RNAs that regulate the transmission of cellular
information through mitotic divisions without changing DNA sequences. The Piwi protein physically and
functionally interacts with small non-coding piRNAs and is required for germline stem cell division. The
Polycomb Group proteins associate with long non-coding RNAs and critically impact development of
various organ and tissue systems. We employ a multidisciplinary approach to determine how Piwi and
Polycomb Group proteins impact stem cells and how their dysfunction contributes to human diseases.
The student will utilize Drosophila or mammalian ES cells as the model system to characterize how
epigenetic factors influence the maintenance and/or differentiation of stem cells. The student will join a
highly enthusiastic and collaborative team and learn biochemical and cell biological techniques that
include DNA and RNA purification, protein extract preparation, immunofluorescence microscopy, cell
culturing and genetic techniques. The student will use these techniques to complete scientific projects,
learn critical scientific thinking, and eventually plan and carry out their own projects.
Jian Zuo, PhD
Member
Department: Developmental Neurobiology
Epigenetics of hair cell development and regeneration in the mouse cochlea
Hearing loss is the third most common health impairment and the most common
occupational illness in the United States. Many things contribute to loss of hearing
including aging, illness, acoustic trauma, and genetic predisposition. Additionally, the mammalian
auditory mechanosensory cells have repeatedly been shown to be susceptible to ototoxicity from a
multitude of drugs including aminoglycoside antibiotics, loop diuretics, platinum-based chemotherapy
agents, and a number of non-steroidal anti-inflammatory drugs (NSAIDS). Unfortunately unlike nonmammalian vertebrates, mammals are unable to regenerate damaged auditory mechanosensory cells
which results in permanent hearing loss.
Since epigenetic regulation of gene expression is a cornerstone of normal development, regeneration,
and cellular reprogramming, one focus of the Zuo lab is to analyze the epigenetic events that take place
during inner ear development to better understand why the mammalian inner ear is unable to
regenerate damaged auditory mechanosensory cells. This project will utilize genetic mouse models
together with various techniques such as drug delivery, immunofluorescence, confocal microscopy,
auditory brainstem response (ABR), quantitative polymerase chain reaction (qPCR), and chromatin
immunoprecipitation (ChIP). A basic understanding of genetics would be helpful but is not required.
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Xinwei Cao, PhD
Assistant Member
Department: Developmental Neurobiology
Our brain is the most complex organ in our body. It controls our bodily functions and
interprets the world around us through our senses. It defines us as human beings
through our memories and our ability to plan for the future. Fundamental to brain
development are neural stem/progenitor cells, which give rise to neurons and glia, the
building blocks of a mature brain. Our lab seeks to understand how neural stem/progenitor cells are
regulated so they can give rise to the right number and type of neurons and glia. Understanding this
question will help us decipher the cause of some neural developmental disorders (such as microcephaly:
small brain), the cause of certain brain tumors, and the genetic changes leading to brain size increase
during evolution.
We mainly use the mouse brain as a model to tackle our questions because many fundamental
mechanisms controlling human brain development are conserved in the mouse brain. We have
generated mouse mutants with various brain development defects. We use molecular biology, cell
biology, histology, and biochemistry approaches to understand how a gene, protein, or signaling
pathway affects the cellular behaviors of neural stem/progenitor cells and how the behaviors of neural
stem/progenitor cells influence the overall structure and composition of the brain.
We welcome students with deep interest and curiosity in biology to work in our lab. The student should
have basic knowledge in general biology, molecular biology, cell biology, biochemistry, and genetics. We
expect the student to be self-motivated, proactive, intelligent, and hard-working. As learning is the
whole purpose of this program, the student should be willing to learn and should take criticism well.
Fabio Demontis, PhD
Assistant Member
Department: Developmental Neurobiology
The Interconnection of Muscle and Systemic Aging via Myokine Signaling
The progressive loss of skeletal muscle function and mass (sarcopenia) is a serious
feature of aging and a key component of the geriatric syndrome of frailty.
Epidemiological surveys in humans indicate that muscle aging influences the progression of several agerelated diseases in other tissues. However, the signaling pathways involved in this inter-tissue
communication are largely unknown. Recently, skeletal muscle has been recognized as an endocrine
tissue with the capacity to secrete cytokines and growth factors, known as myokines, which can act on
distant tissues. We seek to understand the role of skeletal muscle and myokine signaling in the systemic
regulation of aging. Specifically, we aim to investigate how muscle-specific genetic interventions can
regulate lifespan, the role of myokines in mediating the crosstalk between muscle and other tissues, and
the cellular and molecular responses induced in distant tissues. To address these questions we use
transgenic RNAi screens in the fruit fly Drosophila melanogaster and biochemical, molecular and cellular
approaches to identify and characterize new genes and pathways involved in myokine signaling and its
effects on proteostasis and aging. Overall, these studies will progress our understanding on how
organismal aging is an integrated process resulting from signaling events in muscle and other tissues. For
more information, see: www.stjude.org/demontis.
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Junmin Peng, PhD
Associate Member
Director, Proteomics Facility
Departments: Structural Biology, Developmental Neurobiology
Integrative Proteomics and Metabolomics to Human Diseases
The ultimate goal in biomedical research is to understand the molecular mechanism
of life and disease and to develop rational therapeutic strategies for a cure. For
decades, the main approaches are reductionism methods such as studying one or a few genes. Although
those methods have contributed to our understanding of many basic principles, a comprehensive
picture will not be captured until more integrative approaches are utilized. Recently, efforts in genomics,
proteomics, metabolomics, and bioinformatics have made it possible to study all molecules in biological
systems.
Whereas the advent of next-generation sequencing offers unprecedented opportunities for analyzing
DNAs and RNAs, proteomic and metabolomic studies are independent and complementary to the
genomic analysis. Recent development of nanoscale liquid chromatography coupled with high
resolution tandem mass spectrometry (LC-MS/MS) has enabled highly sensitive profiling of more than
10,000 proteins and thousands of metabolites in mammalian cells. It is a propitious time to carry out
such comprehensive analyses.
To probe cellular pathways dysregulated in human diseases, such as pediatric cancer and Alzheimer’s
disease, we have been collaborating with a number of St. Jude investigators to collect control and
diseased specimens (e.g. tissues and biofluids) from human patients or related animal models. We aim
to measure a range of biomolecules in these samples, including genome, transcriptome, proteome,
phosphoproteome and metabolome. These multiple dimensional data will be integrated for network
analysis to reveal molecular insights of disease development. Successful outcome of these projects will
provide novel molecular targets for clinical diagnosis and therapeutic intervention.
Requirements: Course of Chemistry, Biochemistry or Biology
Lea C. Cunningham, MD
Assistant Member
Department: Bone Marrow Transplant
This project is involved in understanding how the tumor microenvironment (TME)
facilitates the development of cancer. A plethora of studies have demonstrated that
interactions between different cells within the TME and cancer cells are important for
the disease maintenance and aggressiveness of cancer. One of the critical regulatory
elements in the TME is Programmed death 1 (PD-1/CD279), an immune checkpoint protein, which is
responsible for the attenuation of the immune response by blocking T-cell function.
The interaction between PD-1 on the tumor infiltrating lymphocytes (TILs) and its ligand, PD-L1 on
tumors, is associated with poor prognosis and aggressiveness of various cancers. A vast number of
studies have suggested that the PD-1/PD-L1 synapse is an adaptation of the tumor to counteract the
host’s immunological responses. This is further substantiated by the fact that PD-L1 expression is
restricted to regions infiltrated by the TILs. Monoclonal antibodies targeting either PD-1 or PD-L1 have
been developed as potential therapy, and have demonstrated promising results. However, only a subset
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of patients has benefited from this therapy. Furthermore, patients who had initially responded to
therapy, later developed resistance. Consequently, it is imperative to investigate the underlying
mechanism(s) of PD-L1 expression in tumors, and to develop better therapeutic strategies.
Techniques: Cell culture, Western blot, Flow cytometry, DNA and RNA isolation, Chromatin
Immunoprecipitation (ChIP) Assay etc.
Requirements: Basic Biology and Immunology.
Hans-Martin Herz, PhD
Assistant Member
Department: Cell & Molecular Biology
Epigenetic misregulation and enhancer malfunction in cancer and other diseases
Accumulating evidence suggests that epigenetic misregulation lies at the heart of
cancer and disease development. Drosophila Trithorax-related (Trr) and mammalian
mixed lineage leukemia 3 and 4 (MLL3/MLL4, also known as KMT2C/KMT2D) belong to a family of SET
domain-containing proteins, that constitute chromatin-modifying enzymes with histone H3 lysine 4
(H3K4) methyltransferase activity. They form the catalytic core of compositionally and functionally
highly conserved protein complexes known as COMPASS (Complex of proteins associated with Set1).
Recent genome-wide studies have revealed that MLL3 and MLL4 are frequently mutated across a broad
spectrum of solid tumors but also certain lymphomas and that mutations in MLL4 might be the leading
cause for a genetic disease called Kabuki syndrome. Similarly, their Drosophila homolog Trr constitutes a
suppressor of tissue growth. Trr and MLL3/MLL4 in a redundant fashion act as major H3K4
monomethyltransferases on cis-regulatory DNA elements known as enhancers and play a role in
enhancer-mediated processes.
However, despite the importance to maintain Trr/MLL3/MLL4 integrity for proper tissue homeostasis,
little is known about the Trr/MLL3/MLL4-dependent basic mechanisms that mediate tumor suppression
or suppress disease onset in the case of Kabuki syndrome. Based on the role of Trr/MLL3/MLL4 in
enhancer-associated H3K4 monomethylation, we hypothesize that changes in the enhancer landscape
of MLL3 and/or MLL4 mutant cancers or of MLL4 mutant patients with Kabuki syndrome might be a
leading cause of tumorigenesis and pathogenesis in Kabuki syndrome. With this in mind, we want to
study Trr/MLL3/MLL4 as a “proof of principle” to gain general mechanistic insight into their role as
epigenetic regulators with a particular focus on Trr/MLL3/MLL4-dependent enhancer-mediated
processes in cancer and other diseases such as Kabuki syndrome. To this end we are utilizing both
Drosophila and mammalian cell culture systems to apply general and novel genome-wide highthroughput sequencing techniques in combination with genetic approaches in Drosophila and
biochemical in vitro studies. Based on our newly gained insight on Trr/MLL3/MLL4 function as a “case
study”, we envision as the next step to start targeted pharmacological and even gene therapeutic
approaches in MLL3 or MLL4 mutant cancers and to apply similar principles to other disease-relevant
epigenetic regulators.
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Stacy Ogden, PhD
Assistant Member
Department: Cell & Molecular Biology
Research in the Ogden lab is focused on the Hedgehog (Hh) signal transduction
pathway, a crucial regulator of developmental patterning that is commonly corrupted
in cancer. Inappropriate activation of Hh signaling is causative in brain and skin cancer,
and is frequently activated in cancers of the colon, breast, lung and blood. We utilize
model systems including Drosophila (fruit fly) genetics, chick neural tube development and mouse cell
culture to understand how Hh signaling is regulated during normal development, and use this
information to identify chemotherapeutic targets to silence aberrant pathway activity in disease.
Students participating in the Rhodes Summer Plus Program will choose from projects focused on: i)
biochemical interrogation of Hh pathway activity through cell culture, sub-cellular fractionation, protein
purification and western blot analysis; ii) cell biological examination of Hh signaling utilizing fluorescence
and electron microscopy; or iii) genetic analysis of Hh regulated developmental processes using
Drosophila and chick model systems. Students will be paired with a postdoctoral fellow to begin their
studies, and over time transition to semi-independent research activity. Upon completion of their
studies, students will have developed a set of basic laboratory research skills, gained an understanding
of how to manage an independent research project and will likely have contributed to the publication of
a laboratory research study.
Scott E. Snyder, PhD
Associate Member
Director, Molecular Imaging Research
Departments: Radiological Sciences, Chemical Biology & Therapeutics
The principal focus of our efforts in Molecular Imaging Research is the development of
novel radiopharmaceuticals and imaging methods for the evaluation and management
of children with tumors using positron emission tomography (PET). PET is a medical
imaging method that can be used to investigate specific aspects of tumor biochemistry and
pathophysiology.
Individual projects combine aspects of Organic Chemistry, Radiochemistry,
Biochemistry and Pharmacology and internship opportunities are available in any or all of these areas. A
typical team project involves the synthesis of precursor molecules for radiolabeling and analytical
standards, determination of optimal conditions for radiolabeling with carbon-11, fluorine-18 or other
PET radionuclides, biochemical evaluation of the mechanism of action of the new radiopharmaceutical
and biological testing in animal models of human disease. Trainees can be involved in any or all of these
aspects. Projects will involve some handling of radioactivity and experimental animals. Students are
encouraged, but not required, to participate in these activities. Students with either chemistry or
biochemistry background are encouraged to apply.
Specific research projects include: a) development, in collaboration with researchers at the University of
Nebraska, of fluorine-18 labeled agents for imaging solid tumors, b) radiolabeling and biological testing
of antibodies and antibody-drug conjugates to facilitate novel therapeutic development, c) biological
evaluation of a new radiotracer for monitoring mitochondrial function, and d) design of radiotracers for
measuring tumor response to therapy.
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Jinghui Zhang, PhD
Member
Chair, Department of Computational Biology
Research in the Department of Computational Biology focuses on understanding the
genetic and epigenetic landscape of pediatric cancer through the development of
novel approaches that integrate whole‐genome sequencing data with RNA
sequencing, copy number variation, structural variation, telomere content and gene
expression data. This work combines large‐scale genomic data with the development or application of
computational algorithms and visualization tools to provide high‐quality analysis to gain novel biological
insight in the genetic or epigenetic changes in the cancer genome. Using this approach, we have
characterized the genomic landscape of over 2000 pediatric cancers. These have included 700 pediatric
tumors and matched non‐tumor germline samples as part of the St. Jude Children's Research Hospital‐
Washington University Pediatric Cancer Genome Project (PCGP). This rich data set enables us to explore
additional genetic architecture that can be used for other genetic research initiatives. Specifically, we
are interested in exploring the possibility of determining the phase of haplotypes based on the allelic
imbalance patterns observed in the tumor genome. This information will be highly useful for
determining linkage disequilibrium important for genetic studies for complex diseases including cancer.
Furthermore, the information can be used to evaluate compound heterozygosity for closely linked loci
to determine the genetic inheritance pattern.
The Rhodes Summer Plus student will participate in the above mentioned research. In particular, a
student with solid training in computer science and a general knowledge about genetics will develop
new approaches to identify haplotypes from tumor genomes by analyzing the allelic imbalance signature
of a paired germline sample. A qualified student shall be able to use the computer cluster and the linux
environment (or with minimum training), has strong motivation for research, has a demonstrated track
record for solving problem through hard work with minimum supervision, capable of exploring new
analytical approach, and has scientific curiosity or training (preferred) in genetics.
Amber Smith, PhD
Research Associate
Department: Infectious Diseases
Mathematical Modeling of Biological Systems
Mathematical modeling is a fantastic tool used to uncover the mechanisms that drive
diseases, such as an infection or cancer. In my laboratory, we use mathematical
models to study the biology of infectious diseases. We focus on the pathogenesis of influenza and
Streptococcus pneumoniae using a data-driven, population-based differential equation modeling
approach. We collect our own data from experimental infections in mice and use mathematics to extract
information about the infection since the biology is quite complex. Theoretical models are excellent
tools for this since they can help us detail the rates that these pathogens infect and spread in the
respiratory tract and how the host immune system responds in a way that an experiment cannot. They
can also help us identify and evaluate treatment options, make predictions about infection mechanisms
and generate hypotheses to test experimentally. The methods we use to study these infections can be
applied to a wide array of other diseases, including cancer.
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As a Rhodes Summer-Plus student in my group, you will learn/apply skills such as how to build a model,
parameterize it using data, simulate the resulting dynamics, and analyze the behavior. You will gain a
foundation for the underlying biology and learn how to design experiments based on your model's
predictions. A strong background in mathematics, completion of ordinary differential equations, and an
interest in either microbiology or cancer biology are preferred.
Hans Haecker, MD, PhD
Associate Member
Department: Infectious Diseases
Signal transduction in innate immune cells and Inflammation
Our lab focuses on the innate immune system, which represents the first line host
defense against infections and also orchestrates other parts of the immune system for
more sophisticated immune responses as required during virus infections and against cancer.
Physiologically, innate immune cells (e.g. macrophages) detect pathogens using specific cell surface
receptors, including Toll-like receptors, which trigger cell activation via partially defined signal
transduction pathways that eventually mediate inflammation. Inflammation is an overall complex
process, which entails the recruitment of other immune cells helping to eradicate the pathogen, in part
by production of cytotoxic substances. Once the pathogen is eliminated, inflammation resolves. While
inflammation in principle is a physiological process, it needs to be tightly controlled in order to prevent
tissue injury as observed in different human diseases, including more systemic syndromes, such as
systemic lupus erythematosus (SLE), or more localized diseases, such as psoriatic skin inflammation
(psoriasis). While the pathogenic mechanisms involved are merely defined, such diseases inflict
significant health problems to affected individuals and may result, particularly if left untreated, even in
death.
Based on quantitative mass spectrometry, we have identified more recently a protein in the TLR
signaling pathways called ABIN1, whose loss of function results in two major inflammatory diseases, i.e.
mentioned SLE and psoriasis, both in humans and (experimentally) in mice. Obviously, this protein has
essential anti-inflammatory functions. Still, its molecular mechanism is only partially understood (PNAS
2011, Zhou et al, PMID: 22011580). This project will investigate the molecular mechanism how ABIN1
controls TLR-induced inflammation in order to prevent inflammatory disease. Experimentally, we take
advantage not only of established genetically engineered mice lacking ABIN1, but also a more recently
developed technique to immortalize immune cell progenitors conditionally, which allows us to
investigate signal transduction and gene regulation in relevant immune cells (Nature Methods 2013,
Redecke et al, PMID: 23749299). Techniques used in this project include basic protein biochemistry,
such as immuno-blotting and immuno-precipitation, cell culture (of different cell lines, including
hematopoietic progenitor cells), basic molecular biology techniques (‘cloning’, generation of expression
vectors), retrovirus production (for delivery of genes into cells) and cell microscopy (including confocal
fluorescence based microscopy).
Results from this study will provide important information on how inflammation is counterbalanced on a
molecular level with likely therapeutic implications for human diseases.
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Deena Levine, MD
Assistant Member
Department: Oncology
Patterns of End-of-Life Care in Children with Cancer
The Quality of Life service at St Jude was created in 2007 as a consult service aiming to
“provide each child living with or dying from a catastrophic illness with state-of -the-art
patient and family-centered physical, emotional, and spiritual care with the goal to attend suffering,
promote healing, and improve quality of life.” We have catalogued the progress of the quality of life
service by way of an institutional database tracking key metrics of patient characteristics and care. In
this project we seek to evaluate outcomes and symptoms in children with cancer and compare patterns
of end-of-life care after implementation of a dedicated institutional pediatric palliative care (PC) service.
The student will assist in a retrospective cohort study of children who died of cancer treated at St. Jude
Children's Research Hospital, before and after implementation of the institutional QoL/PC service in
January 2007. The student will be mentored and gain experience in clinical research, chart review, data
extraction, database management, statistical analysis and scientific writing. Previous similar student
work in our department has led to significant findings and peer reviewed publications. We look forward
to working together soon!
Mark Hatley, MD, PhD
Assistant Member
Department: Oncology
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood.
Despite three decades of rigorous and intensive clinical trials the overall survival of
RMS has not increased from 70%. There are two histologic types of RMS, embryonal
and alveolar. Alveolar RMS (ARMS) has the worst outcome, is more prone to metastasis, and is driven
by the translocation t(2;13) that results in production of a PAX3-FOXO1 fusion protein. The PAX3-FOXO1
fusion protein acts as a rogue transcription factor that drives many of the genes participating in the
pathogenesis. Many of these PAX3-FOXO1 target genes including (MET, FGFR4, ALK) have become the
targets of therapeutic trials for targeted agents in ARMS. The role of another class of genes called
microRNAs has been unexplored.
MicroRNAs are small, 19 to 25 base pair non-coding RNAs that negatively regulate gene expression
through interactions with the 3’ untranslated region of target genes. MicroRNA binding to the 3’
untranslated region of the target gene either results in the destruction of the mRNA or represses the
translation of the mRNA. MicroRNAs have been shown to participate in the pathogenesis of many
tumors, but the role in ARMS remains to be elucidated. We have profiled the expression of microRNAs
in ERMS, ARMS and normal skeletal muscle progenitors and illustrated that each has a very distinct
pattern of miRNA expression. The lab has focused on the role of the differentially expressed microRNAs
in the pathogenesis of ARMS. Students working in the lab will explore the function of differentially
expressed miRNAs in ARMS pathogenesis as well as normal skeletal muscle differentiation. This project
will give the student a very broad exposure to techniques including molecular cloning, cell culture, viral
expression systems, luminescence reporter assays, apoptosis assays, flow cytometery, northern and
western blotting, muscle differentiation assays, real time PCR, and xenograft models. No technical
prerequisites required just a willingness to learn. The students will participate and present in weekly lab
journal club and lab meeting. The laboratory has three experienced postdoctoral fellows and a
seasoned lab manager/technician that will facilitate a nurturing and educational environment.
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Weiguang Yao, PhD
Assistant Member
Department: Radiation Oncology
Random-walk-model based proton computed tomography
X-ray computed tomography, commonly known as CT, is currently the only image for
radiation dose calculation in radiation treatment planning. CT indicates the
information of interactions between the photon and the traversed medium, and thus the volumetric CT
image provides direct information for x-ray radiation dose prediction in the volume, i.e. the patient
body. Another rationale for CT to be used in the dose calculation is the rather energy independence of
the stopping power of the photon in the medium. This makes the dose calculation accurate of the megavoltage photons, used in treatment, from the kilo-voltage photons, used in CT. The voxel in the
volumetric CT image is expressed by Hounsfield units, which is the function of the electron density of
the medium at the voxel and the photon energy. With known photon energy, one can calculate the
electron density from the Hounsfield units. The electron density of the medium determines the
radiation dose.
The interactions of protons with the medium are different from those of photons, and the stopping
power of the proton in the medium is highly energy dependent. Proton is charged but photon is not.
Thus, limits exist when x-ray CT is used for proton dose calculation, which requires the physical density,
electron density and chemical components of the medium. It is challenging to determine these
parameters from the Hounsfield units. Intuitively, use of proton computed tomography (pCT) can solve
this problem. Unfortunately, the pioneer work has discovered that the pCT image is very blurred due to
the lateral multiple-coulomb scatter.
We have studied random walk model for proton dose calculation. The similar analysis will be applied to
improve the image quality of pCT. The student will use Monte Carlo software to generate the
projections of protons after designed phantoms, apply random walk model to extract required
information from the projections, and do the image reconstruction. The student also has chance to
acquire the real proton projections in our proton treatment center. The student is expected to have
some knowledge of radiation physics and some experience of scientific computing.
Charles Mullighan, MBBS, MSc,MD
Member
Co-director, Hematological Malignancies Program
Department: Pathology
Functional modeling of novel alterations in acute erythroid leukemia
Background
We recently discovered deregulation of the erythropoietin receptor (EPOR), as an important factor
influencing B-lymphoid malignancies (accepted) and hypothesized that abnormal regulation of EPOR
signaling could be also involved in hematological proliferative malignancies characterized by
erythrocytosis. Among these, acute erythroid leukemia (AEL), an uncommon type of acute myeloid
leukemia (AML), characterized by a predominantly erythroid cell proliferation in the bone marrow, poor
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risk cytogenetics and poor survival, was a logical candidate since overexpression of EPOR has been
described in AEL cell lines and primary samples.
Through an international study we collected eighty-seven AEL cases whose diagnosis was centrally
confirmed at St Jude Children’s Research Hospital. Primary samples were from 64 adults (74%) and 23
children (26%) with AEL. Moreover, two established AEL cell lines (HEL and TF-1) were included in the
study and used as model of AEL in vitro and in vivo.
AEL primary samples and TF-1 and HEL AEL cell lines were analyzed by mRNA-seq, whole exome
sequencing and SNP 6.0 microarray to 1) identify recurrent chimeric transcripts, 2) identify any other
recurrent genetic variants and 3) copy number changes that may be involved in the leukemogenesis of
AEL cases.
Hypothesis
Alterations of erythroid signaling and transcriptional pathways are a hallmark of acute erythroid
leukemia.
Overall aims
AEL is a morphologically distinct, infrequent (<5%) AML designed as M6 in the French-American-British
classification. Diagnosis is often difficult and still mainly based on morphology due to the lack of a
recurrent cytogenetic abnormality. The prognosis is terribly poor both in children and adult patients
suggesting a compelling need to improve our understanding of genetic alterations involved in the
pathogenesis of AEL. The overall goal of this project is to dissect the genomic background of AEL and to
develop models for functional characterization.
Specific aims
By RNA-seq screening chimeric transcripts were identified in 56% and 54% of adult and pediatric cases,
respectively. Interestingly, fusion genes involving erythroid regulators (e.g. MYB-GATA1, ZBTB7A-BCR,
and NFIX-ZNF93), chromatin modifiers (ZEB1-KDMC4, NUP98-KDM5A, NPM1-MLF4) or cytokine
receptors (EPOR-PKHD1L1, CDC37-IL27RA, ALP2-EPOR) were detected. Whole-exome sequencing
identified single nucleotide variants and/or indels in all cases, with TP53 being the most mutated gene
(25%).
The specific aim of this project is to unravel the pathogenetic role of the most frequent and relevant
genetic alterations in AEL. Novel gene fusions or mutated genes will be cloned in the murine stem cell
virus (MSCV)-internal ribosome entry site - green fluorescence protein vector (MIG) and will be
expressed in wild-type and Tp53-/- mouse lineage negative hematopoietic stem cells (Lin- HSC).
Transduced Lin- HSC will be used in colony forming unit assays for both myeloid and erythroid lineages
to investigate the transformative properties and clonal abilities of genetic alterations and in
transplantation of lethally irradiated C57Bl/6 mouse to assess the leukemia development and drug
sensitivity.
Prerequisite skills needed
Good experience in molecular and cellular biology techniques including extraction of nucleic acids, PCR,
PCR purification, growing of cells in culture.